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- PDB-2uz9: Human guanine deaminase (guaD) in complex with zinc and its produ... -

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Basic information

Entry
Database: PDB / ID: 2uz9
TitleHuman guanine deaminase (guaD) in complex with zinc and its product Xanthine.
ComponentsGUANINE DEAMINASE
KeywordsHYDROLASE / ZINC / PURINE METABOLISM / GUANINE AMINOHYDROLASE
Function / homology
Function and homology information


guanine deaminase / guanine deaminase activity / guanine catabolic process / deoxyguanosine catabolic process / dGMP catabolic process / GMP catabolic process / amide catabolic process / guanine metabolic process / Purine catabolism / allantoin metabolic process ...guanine deaminase / guanine deaminase activity / guanine catabolic process / deoxyguanosine catabolic process / dGMP catabolic process / GMP catabolic process / amide catabolic process / guanine metabolic process / Purine catabolism / allantoin metabolic process / nucleobase-containing compound metabolic process / nervous system development / zinc ion binding / cytosol
Similarity search - Function
Guanine deaminase / Urease, subunit C; domain 1 / Urease, subunit C, domain 1 / Amidohydrolase family / Metal-dependent hydrolase, composite domain superfamily / Amidohydrolase-related / Metal-dependent hydrolases / Metal-dependent hydrolase / Roll / TIM Barrel ...Guanine deaminase / Urease, subunit C; domain 1 / Urease, subunit C, domain 1 / Amidohydrolase family / Metal-dependent hydrolase, composite domain superfamily / Amidohydrolase-related / Metal-dependent hydrolases / Metal-dependent hydrolase / Roll / TIM Barrel / Alpha-Beta Barrel / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
XANTHINE / Guanine deaminase
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsMoche, M. / Welin, M. / Arrowsmith, C. / Berglund, H. / Busam, R. / Collins, R. / Dahlgren, L.G. / Edwards, A. / Flodin, S. / Flores, A. ...Moche, M. / Welin, M. / Arrowsmith, C. / Berglund, H. / Busam, R. / Collins, R. / Dahlgren, L.G. / Edwards, A. / Flodin, S. / Flores, A. / Graslund, S. / Hammarstrom, M. / Hallberg, B.M. / Holmberg-Schiavone, L. / Johansson, I. / Kallas, A. / Karlberg, T. / Kotenyova, T. / Lehtio, L. / Nyman, T. / Ogg, D. / Persson, C. / Sagemark, J. / Stenmark, P. / Sundstrom, M. / Thorsell, A.G. / van den berg, S. / Weigelt, J. / Nordlund, P. / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: Human Guanine Deaminase (Guad) in Complex with Zinc and its Product Xhantine
Authors: Moche, M. / Welin, M. / Arrowsmith, C. / Berglund, H. / Busam, R. / Collins, R. / Dahlgren, L.G. / Edwards, A. / Flodin, S. / Flores, A. / Graslund, S. / Hammarstrom, M. / Hallberg, B.M. / ...Authors: Moche, M. / Welin, M. / Arrowsmith, C. / Berglund, H. / Busam, R. / Collins, R. / Dahlgren, L.G. / Edwards, A. / Flodin, S. / Flores, A. / Graslund, S. / Hammarstrom, M. / Hallberg, B.M. / Holmberg-Schiavone, L. / Johansson, I. / Kallas, A. / Karlberg, T. / Kotenyova, T. / Lehtio, L. / Nyman, T. / Ogg, D. / Persson, C. / Sagemark, J. / Stenmark, P. / Sundstrom, M. / Thorsell, A.G. / Van Den Berg, S. / Weigelt, J. / Nordlund, P.
History
DepositionApr 26, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 8, 2007Provider: repository / Type: Initial release
Revision 1.1Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AB" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 9-STRANDED BARREL THIS IS REPRESENTED BY A 10-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: GUANINE DEAMINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,8383
Polymers53,6211
Non-polymers2182
Water3,477193
1
A: GUANINE DEAMINASE
hetero molecules

A: GUANINE DEAMINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,6766
Polymers107,2412
Non-polymers4354
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_554-x,y,-z-11
Buried area5250 Å2
ΔGint-21.5 kcal/mol
Surface area37460 Å2
MethodPQS
Unit cell
Length a, b, c (Å)91.735, 85.713, 78.960
Angle α, β, γ (deg.)90.00, 116.49, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein GUANINE DEAMINASE / / GUANASE / GUANINE AMINASE / GUANINE AMINOHYDROLASE / GAH / P51-NEDASIN


Mass: 53620.555 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: THE PROTEIN CHAIN CONTAINS A HEXAHISTIDINE TAIL IN THE N-TERMINUS
Source: (gene. exp.) HOMO SAPIENS (human) / Description: MAMMALIAN GENE COLLECTION (MGC) / Plasmid: PNIC-BSA4 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9Y2T3, guanine deaminase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-XAN / XANTHINE / Xanthine


Mass: 152.111 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H4N4O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 193 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsOUR CLONED CONSTRUCT CONTAINS A HEXAHISTIDINE TAG AND A LINKER SEQUENCE IN THE N-TERMINUS ...OUR CLONED CONSTRUCT CONTAINS A HEXAHISTIDINE TAG AND A LINKER SEQUENCE IN THE N-TERMINUS (MHHHHHHSSGVDLGTENLYFQS).

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.65 Å3/Da / Density % sol: 53.14 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.984
DetectorType: MARRESEARCH / Detector: CCD / Date: Jan 17, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.984 Å / Relative weight: 1
ReflectionResolution: 2.3→20 Å / Num. obs: 24361 / % possible obs: 99.8 % / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 13.3
Reflection shellResolution: 2.3→2.42 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.51 / Mean I/σ(I) obs: 2.5 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2I9U

2i9u


Resolution: 2.3→30 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.934 / SU B: 6.542 / SU ML: 0.158 / Cross valid method: THROUGHOUT / ESU R: 0.269 / ESU R Free: 0.209 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.222 1241 5.1 %RANDOM
Rwork0.169 ---
obs0.172 23120 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.93 Å2
Baniso -1Baniso -2Baniso -3
1--0.99 Å20 Å20.25 Å2
2---1.73 Å20 Å2
3---2.94 Å2
Refinement stepCycle: LAST / Resolution: 2.3→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3521 0 12 193 3726
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0223637
X-RAY DIFFRACTIONr_bond_other_d0.0010.022442
X-RAY DIFFRACTIONr_angle_refined_deg1.3661.9564926
X-RAY DIFFRACTIONr_angle_other_deg0.95335960
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5925449
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.64124.419172
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.0215629
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.0951518
X-RAY DIFFRACTIONr_chiral_restr0.0830.2549
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.024063
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02751
X-RAY DIFFRACTIONr_nbd_refined0.1940.2764
X-RAY DIFFRACTIONr_nbd_other0.1920.22604
X-RAY DIFFRACTIONr_nbtor_refined0.1780.21750
X-RAY DIFFRACTIONr_nbtor_other0.0870.21890
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.160.2211
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1780.211
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2610.251
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1490.29
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.16422888
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.50833598
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.15141647
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.9351328
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.354 92
Rwork0.232 1681

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